BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354854.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 37,463,832 number of mapped reads = 36,839,135 (98.33%) number of supplementary alignments = 699,234 (1.87%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 18,493,007 number of mapped paired reads (second in pair) = 18,346,128 number of mapped paired reads (both in pair) = 36,641,508 number of mapped paired reads (singletons) = 197,627 number of mapped bases = 5,130,852,192 bp number of sequenced bases = 5,128,248,313 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,322,019 duplication rate = 59.7% >>>>>>> Insert size mean insert size = 162,784.2637 std insert size = 4,579,579.7632 median insert size = 320 >>>>>>> Mapping quality mean mapping quality = 54.0231 >>>>>>> ACTG content number of A's = 1,479,331,992 bp (28.85%) number of C's = 1,064,795,527 bp (20.76%) number of T's = 1,487,754,620 bp (29.01%) number of G's = 1,096,326,892 bp (21.38%) number of N's = 39,282 bp (0%) GC percentage = 42.14% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 43,761,609 number of insertions = 859,598 mapped reads with insertion percentage = 2.17% number of deletions = 914,193 mapped reads with deletion percentage = 2.36% homopolymer indels = 43.61% >>>>>>> Coverage mean coverageData = 1.6574X std coverageData = 36.3111X There is a 43.81% of reference with a coverageData >= 1X There is a 33.55% of reference with a coverageData >= 2X There is a 23.01% of reference with a coverageData >= 3X There is a 16.93% of reference with a coverageData >= 4X There is a 11.24% of reference with a coverageData >= 5X There is a 8.14% of reference with a coverageData >= 6X There is a 5.35% of reference with a coverageData >= 7X There is a 3.85% of reference with a coverageData >= 8X There is a 2.52% of reference with a coverageData >= 9X There is a 1.81% of reference with a coverageData >= 10X There is a 1.2% of reference with a coverageData >= 11X There is a 0.86% of reference with a coverageData >= 12X There is a 0.58% of reference with a coverageData >= 13X There is a 0.42% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.22% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 414361918 1.6624308350268864 51.21532922766431 chr2 243199373 452890545 1.8622192130404875 96.4038376258306 chr3 198022430 331524694 1.6741774858534966 3.013213962925285 chr4 191154276 343910743 1.7991266018030379 27.27917396735204 chr5 180915260 305035774 1.6860698981390514 2.8071968841666606 chr6 171115067 284931459 1.6651453550843656 6.6950375828156545 chr7 159138663 280884180 1.7650278989713517 28.80310981341095 chr8 146364022 251537964 1.7185778346539289 18.596175785630177 chr9 141213431 221944871 1.5716980277888724 31.094281460002776 chr10 135534747 280354874 2.068509221476615 52.270636651979 chr11 135006516 262209659 1.9422000268490744 8.92844496642749 chr12 133851895 221108055 1.6518858772974414 2.715294765998688 chr13 115169878 158487141 1.37611625324462 2.4410613484929113 chr14 107349540 153405351 1.429026626476462 4.375148580865545 chr15 102531392 143245895 1.3970930483417214 2.469974138053911 chr16 90354753 157512803 1.743270805023395 10.404654470038698 chr17 81195210 140603892 1.7316771765230978 10.495923507554068 chr18 78077248 142286894 1.8223861322571204 24.677064100919804 chr19 59128983 104118898 1.7608775378396073 28.758429746954366 chr20 63025520 106646168 1.692110878260108 9.172086988222572 chr21 48129895 72557137 1.5075274317552532 14.151011461181575 chr22 51304566 53933322 1.0512382465139654 4.8310304777616295 chrMT 16571 44397376 2679.2212902057813 426.06377887804496 chrX 155270560 138199450 0.8900557195130874 3.257851552863854 chrY 59373566 64763129 1.0907737796985277 30.421182188014512